Reporting using Rmarkdown
Taro Mieno
2022-01-28
1 Basic illustrations
1.1 R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.
When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
summary(cars)## speed dist
## Min. : 4.0 Min. : 2.00
## 1st Qu.:12.0 1st Qu.: 26.00
## Median :15.0 Median : 36.00
## Mean :15.4 Mean : 42.98
## 3rd Qu.:19.0 3rd Qu.: 56.00
## Max. :25.0 Max. :120.001.2 Including Plots
You can also embed plots, for example:
Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.
1.3 Including a table
| Sepal.Length | Sepal.Width | Petal.Length | Petal.Width | Species |
|---|---|---|---|---|
| 5.1 | 3.5 | 1.4 | 0.2 | setosa |
| 4.9 | 3.0 | 1.4 | 0.2 | setosa |
| 4.7 | 3.2 | 1.3 | 0.2 | setosa |
| 4.6 | 3.1 | 1.5 | 0.2 | setosa |
| 5.0 | 3.6 | 1.4 | 0.2 | setosa |
1.4 Inline r code
The average yield is 104.5701349.
2 Markdown basics (level 1 header)
2.1 level 2 header
2.1.1 level 3 header
See the source rmd file:
- list item 1
- list item 2
- list item 3
- italics
- bold
code(do not put r right after the first tick mark)- inline math: I hate math. What does this \(\int_a^b f(x)dx\) even mean?
- math: \[\sum_{i=1}^n x_i/n\]
- link: Markdown basics
- citationL: The best resource to learn how to use Rmarkdown is [@xie2018r].
3 Chunk options
3.1 echo and eval
R code and results
## speed dist
## Min. : 4.0 Min. : 2.00
## 1st Qu.:12.0 1st Qu.: 26.00
## Median :15.0 Median : 36.00
## Mean :15.4 Mean : 42.98
## 3rd Qu.:19.0 3rd Qu.: 56.00
## Max. :25.0 Max. :120.00R code suppressed
## speed dist
## Min. : 4.0 Min. : 2.00
## 1st Qu.:12.0 1st Qu.: 26.00
## Median :15.0 Median : 36.00
## Mean :15.4 Mean : 42.98
## 3rd Qu.:19.0 3rd Qu.: 56.00
## Max. :25.0 Max. :120.00Only R code (R code was not evaluated)
Both R codes and results not shown
3.2 messages and warnings
3.2.1 both messages and warnings
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──## ✓ ggplot2 3.3.5 ✓ purrr 0.3.4
## ✓ tibble 3.1.6 ✓ dplyr 1.0.6
## ✓ tidyr 1.1.3 ✓ stringr 1.4.0
## ✓ readr 1.4.0 ✓ forcats 0.5.0## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()3.2.2 messages suppressed
3.2.3 both messages and warnings suppressed
3.3 results
No results are shown.
But, this shows the above code was evaluated and object a was created.
## [1] 0.350349978 0.462961236 0.113930023 0.174954225 0.170794062 0.692183580
## [7] 0.594846918 0.108901789 0.192909662 0.767943610 0.643715249 0.204480004
## [13] 0.811863986 0.250452001 0.592385723 0.455391258 0.156572630 0.446857813
## [19] 0.379850575 0.320651675 0.894127643 0.006882706 0.768682064 0.998470782
## [25] 0.264791884 0.678178260 0.694719936 0.930123904 0.034711960 0.699248383
## [31] 0.946193314 0.142036333 0.561562106 0.049861000 0.816663454 0.820352075
## [37] 0.452741143 0.063522938 0.722392725 0.720759323 0.064292517 0.242588780
## [43] 0.794172431 0.823621822 0.730496784 0.396951622 0.907722458 0.713651714
## [49] 0.804905373 0.847965190 0.541036627 0.564436201 0.407830226 0.667268012
## [55] 0.277183371 0.679271965 0.346870973 0.692321878 0.129938756 0.921728347
## [61] 0.914437613 0.771757945 0.887645973 0.414095334 0.484922018 0.901446478
## [67] 0.731437017 0.268911513 0.553278452 0.158925594 0.451630498 0.121996131
## [73] 0.510852352 0.424533339 0.339447412 0.183757645 0.459291716 0.912609611
## [79] 0.383858969 0.896177272 0.801157310 0.009233527 0.341500588 0.542254291
## [85] 0.158979408 0.932199056 0.706849628 0.229528976 0.117932425 0.173632829
## [91] 0.413076432 0.509131103 0.517910171 0.586827479 0.564893162 0.210912060
## [97] 0.281101293 0.010776010 0.478054321 0.6235973973.4 include = FALSE
No results are shown.
But, this shows the above code was evaluated and object a was created.
## [1] 0.432755550 0.165662263 0.494497007 0.513510063 0.389520589 0.825907012
## [7] 0.158607424 0.517705345 0.742594786 0.850320895 0.766178553 0.895417884
## [13] 0.677629195 0.193991130 0.569156493 0.236197319 0.646050078 0.963014559
## [19] 0.146671619 0.240249194 0.215842424 0.692349957 0.388789160 0.268796646
## [25] 0.455459617 0.504718999 0.998614138 0.894502518 0.043829975 0.342263919
## [31] 0.755652204 0.024545879 0.153506475 0.401038759 0.368672557 0.387309436
## [37] 0.198668671 0.334165278 0.874041097 0.125209298 0.794027489 0.921342529
## [43] 0.718627725 0.813465691 0.558696928 0.404679572 0.254410440 0.136160392
## [49] 0.931873044 0.949969484 0.332159783 0.605401500 0.300705315 0.720055781
## [55] 0.035243671 0.395915923 0.962534831 0.295649291 0.319097202 0.589422338
## [61] 0.005535505 0.965867588 0.621694700 0.323932148 0.383581850 0.080525472
## [67] 0.167485865 0.273585262 0.998870753 0.065502524 0.155752643 0.689883248
## [73] 0.905547015 0.215939532 0.202750838 0.006248704 0.378182829 0.282803346
## [79] 0.930805537 0.235225616 0.591660779 0.914137021 0.246989580 0.914661225
## [85] 0.559775507 0.553047433 0.153801772 0.952906096 0.099300105 0.422490828
## [91] 0.831821156 0.024668382 0.535494362 0.039895258 0.810180390 0.988930806
## [97] 0.019438346 0.726748163 0.214647833 0.2471377784 Caching
## [1] 1.500241## [1] 1.5002415 Interactive features: htmlwidgets
5.1 interactive data table
5.2 Interactive time-series data
5.3 Interactive ggplot2 figures
##
## Attaching package: 'plotly'## The following object is masked from 'package:ggplot2':
##
## last_plot## The following object is masked from 'package:stats':
##
## filter## The following object is masked from 'package:graphics':
##
## layout